Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403754 http://www.ncbi.nlm.nih.gov/pubmed/12805271 https://doi.org/10.1101/gr.1180903 |
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ftpubmed:oai:pubmedcentral.nih.gov:403754 2023-05-15T13:39:28+02:00 Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii Saunders, Neil F.W. Thomas, Torsten Curmi, Paul M.G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo 2003-07 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403754 http://www.ncbi.nlm.nih.gov/pubmed/12805271 https://doi.org/10.1101/gr.1180903 en eng Cold Spring Harbor Laboratory Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403754 http://www.ncbi.nlm.nih.gov/pubmed/12805271 http://dx.doi.org/10.1101/gr.1180903 Copyright © 2003, Cold Spring Harbor Laboratory Press Articles Text 2003 ftpubmed https://doi.org/10.1101/gr.1180903 2013-08-29T23:13:21Z We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15°–98°C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60°C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles. Text Antarc* Antarctic PubMed Central (PMC) Antarctic The Antarctic Genome Research 13 7 1580 1588 |
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Articles Saunders, Neil F.W. Thomas, Torsten Curmi, Paul M.G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
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We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15°–98°C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60°C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles. |
format |
Text |
author |
Saunders, Neil F.W. Thomas, Torsten Curmi, Paul M.G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo |
author_facet |
Saunders, Neil F.W. Thomas, Torsten Curmi, Paul M.G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo |
author_sort |
Saunders, Neil F.W. |
title |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_short |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_full |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_fullStr |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_full_unstemmed |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_sort |
mechanisms of thermal adaptation revealed from the genomes of the antarctic archaea methanogenium frigidum and methanococcoides burtonii |
publisher |
Cold Spring Harbor Laboratory Press |
publishDate |
2003 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403754 http://www.ncbi.nlm.nih.gov/pubmed/12805271 https://doi.org/10.1101/gr.1180903 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403754 http://www.ncbi.nlm.nih.gov/pubmed/12805271 http://dx.doi.org/10.1101/gr.1180903 |
op_rights |
Copyright © 2003, Cold Spring Harbor Laboratory Press |
op_doi |
https://doi.org/10.1101/gr.1180903 |
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Genome Research |
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13 |
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7 |
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1580 |
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1588 |
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1766119378491801600 |